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• 5639a09fb9 Add the --with-taxon-at-rank option code to obiannotate Eric Coissac 2023-02-02 16:36:32 +01:00
• 886c5118e3 install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:37:27 +01:00
• a1fbaed6e9 install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:36:55 +01:00
• f0a2744435 install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:23:16 +01:00
• 49e4cefd5b install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:15:59 +01:00
• 5dbf8d6203 remove the g prefix by default Eric Coissac 2023-02-02 13:11:04 +01:00
• 2cb3542d30 adds installation instructions Eric Coissac 2023-02-02 12:42:44 +01:00
• 994da5d710 adds installation instructions Eric Coissac 2023-02-02 12:41:30 +01:00
• 822e584f9a install script with options of install directory and command prefix Eric Coissac 2023-02-02 12:21:49 +01:00
• ab0c93d303 install script with options of install directory and command prefix Eric Coissac 2023-02-02 12:18:04 +01:00
• c0df4357dd install script with options of install directory and command prefix Eric Coissac 2023-02-02 12:16:56 +01:00
• 03b124f400 Patch a bug in MamberSub for primers longer than 32 Eric Coissac 2023-02-01 16:23:14 +01:00
• 7c44243032 Change the URL of the obitools repository Eric Coissac 2023-02-01 08:34:25 +01:00
• e3d4da2859 small things... Eric Coissac 2023-02-01 08:14:29 +01:00
• 3a151fc0a0 updated gitignire Eric Coissac 2023-01-31 23:14:33 +01:00
• 871f22b83d Latest version of the doc in HTML Eric Coissac 2023-01-31 23:04:28 +01:00
• fa6853fca1 Comment profiling code Eric Coissac 2023-01-31 22:39:34 +01:00
• e5835310cc Simplify code of the JSON header formater Eric Coissac 2023-01-31 17:16:55 +01:00
• 57c7187e6d Patch the JSON header formater Eric Coissac 2023-01-31 17:15:10 +01:00
• 9f98075510 Patched version of install script Eric Coissac 2023-01-27 14:50:45 +01:00
• f74c0bd517 First prelease of obiannotate Eric Coissac 2023-01-27 11:35:39 +01:00
• 39b47a32bf Complement on the doc Eric Coissac 2023-01-27 10:49:28 +01:00
• cfddc78161 Patch an aligment bug on obipairing Eric Coissac 2023-01-25 13:22:56 +01:00
• 9b7edf0908 Add an install script to help in installing obitools 4 on Linux or MacOS computers Eric Coissac 2023-01-23 15:44:23 +01:00
• 2d375df94f move the worker class to the obiseq package Eric Coissac 2023-01-22 22:39:13 +01:00
• f97f92df72 rename the iterator class Eric Coissac 2023-01-22 22:04:17 +01:00
• 4592855095 Adds the new version of the doc as a quarto book Eric Coissac 2023-01-17 19:06:14 +01:00
• f873645e8e Remove old bookdown version of the documentation Eric Coissac 2023-01-17 19:02:27 +01:00
• 20b16c0ba1 Force sequence reading to produce lowercase sequences. Adds two columns to the obiclean ratio csv file Eric Coissac 2022-11-22 15:06:09 +01:00
• f4daa7f97f Modify the gitignore Eric Coissac 2022-11-17 12:05:11 +01:00
• 95b28a6612 Beginning of the documentation Eric Coissac 2022-11-17 11:16:12 +01:00
• 29563aa94e Rename the Length methods Len to follow GO standart Eric Coissac 2022-11-17 11:09:58 +01:00
• eb32089305 Refactoring related to iterators Eric Coissac 2022-11-16 17:13:40 +01:00
• 09fc426b67 Refactoring related to iterators Eric Coissac 2022-11-16 17:13:03 +01:00
• 6f853da9df Remove single sequence ierators. Only batch iterators persist Eric Coissac 2022-11-16 10:58:59 +01:00
• f674200a6e FastLCS with maxError=-1 is equivalent to FullLCS. Eric Coissac 2022-11-16 09:57:36 +01:00
• 4375dbd9bb Switxh alignment to the new LCS method and make a copy of the sequences before annotating them to prevent concurrent map access bug Eric Coissac 2022-11-16 09:27:04 +01:00
• 18447e66a7 Patch a critical bug into the CopySlice function. Eric Coissac 2022-11-16 09:24:17 +01:00
• 7f863fb383 Prevens errors on FASTA formating an empty sequence Eric Coissac 2022-11-16 09:22:55 +01:00
• 493c7fddef Adds API documentation Eric Coissac 2022-11-16 09:21:54 +01:00
• abe210d811 Correct option alias name to remove dupplicate Eric Coissac 2022-11-15 08:58:41 +01:00
• 340579f6d7 New version of LCS computation, with abug on alignment length patched patched Eric Coissac 2022-11-15 08:21:46 +01:00
• 18be4becec Add some new packages Eric Coissac 2022-11-14 14:36:04 +01:00
• 0f99f9a6ba First trial of a fastest LCS implementation Eric Coissac 2022-11-14 07:42:15 +01:00
• 6429f24c57 Accellerate a bit LCS computation Eric Coissac 2022-10-27 17:30:55 +02:00
• f3ddac0f50 Small adjustment Eric Coissac 2022-10-27 11:18:44 +02:00
• 8aa323dad5 Add a first version of obitag the successor of ecotag Eric Coissac 2022-10-26 13:16:56 +02:00
• e17d1fbca6 Patch the error message stored in sequences by obimultiplex Eric Coissac 2022-10-17 21:32:24 +02:00
• f8df48338d Several bug in annotation management Eric Coissac 2022-10-12 23:01:47 +02:00
• aae3398701 Replace the CopyMap function by the MustFillMap and adds a InterfaceToIntMap function Eric Coissac 2022-10-12 22:56:38 +02:00
• 58dbdd8698 requires that father.count > son.count Eric Coissac 2022-10-05 09:53:56 +02:00
• d9c18ab0b5 Add a reverse complement worker Eric Coissac 2022-10-05 09:41:59 +02:00
• 935fc31982 Adds the new obicomplement command Eric Coissac 2022-10-05 09:40:09 +02:00
• 7873b90902 Patch a bug in obigrep... Eric Coissac 2022-10-02 20:52:26 +02:00
• 65210755cc Patch reading of annotation from stdin Eric Coissac 2022-09-29 14:48:05 +02:00
• d0f63fda56 add functionalities to the expression predicate evaluations Eric Coissac 2022-09-28 16:13:20 +02:00
• fe5d8e3340 Patch a bug in ngsfilter reading and sample matching Eric Coissac 2022-09-28 14:29:19 +02:00
• ebefa28cc0 Patch memory error related to []byte pool Eric Coissac 2022-09-28 14:28:37 +02:00
• 57ba460929 add the obi_mutation attribute to the sequences Eric Coissac 2022-09-20 22:03:44 +02:00
• da8e3fd7b7 Correct the orientation of the mutation pattern Eric Coissac 2022-09-20 22:03:01 +02:00
• 49b4d97803 Remove HTML escaping to json marshaling Eric Coissac 2022-09-20 22:01:52 +02:00
• 3cd8aabd83 Correct some misspelling in option helps Changes to be committed: modified: pkg/obitools/obiclean/options.go modified: pkg/obitools/obiconvert/options.go Eric Coissac 2022-09-20 21:59:38 +02:00
• f6735a634e Correctly patch the memory leak related to the apatsequence Eric Coissac 2022-09-12 15:19:46 +02:00
• 448f5f83fa Patch a bug in comparison of attibutes during sequence annotation merging Eric Coissac 2022-09-08 07:50:17 +02:00
• 6b8f4490cf Change obiclean algorithm for a better evaluation of ratio Eric Coissac 2022-08-31 20:38:03 +02:00
• 90ba980de6 correct the gml writer Eric Coissac 2022-08-30 10:28:05 +02:00
• cd202ba72e Adds of new modules Eric Coissac 2022-08-23 15:09:51 +02:00
• 91c2ce551d Add new modules Eric Coissac 2022-08-23 15:09:03 +02:00
• d04161a0fb small code refactoring Eric Coissac 2022-08-23 15:08:35 +02:00
• d2f4919bc8 comment out to option that need to be rethought Eric Coissac 2022-08-23 15:07:48 +02:00
• 989e678f6b refactor code and change algorithm used to read from many files Eric Coissac 2022-08-23 15:07:06 +02:00
• bdf317819b Code refactoring Eric Coissac 2022-08-23 11:12:00 +02:00
• 57e0966d35 Adds some documentation Eric Coissac 2022-08-23 11:11:36 +02:00
• 4df99cec5b Chang log package Eric Coissac 2022-08-23 11:10:04 +02:00
• abaede48b5 Refactoring of some code Eric Coissac 2022-08-23 11:07:39 +02:00
• 62968aaa26 patch the Taxid method Eric Coissac 2022-08-23 11:06:51 +02:00
• 1e58c92086 Adds a function to test that a list contains at least one occurrence of an element Eric Coissac 2022-08-23 11:06:28 +02:00
• 5a81525e46 Adds a genbank parser Eric Coissac 2022-08-23 11:04:57 +02:00
• a71e65963b Modify the .gitignore Eric Coissac 2022-08-21 17:53:51 +02:00
• 31c45bf46f Adds documentation and few methods to the BioSequences Eric Coissac 2022-08-21 17:53:19 +02:00
• eca1af9957 Patch a bug on the FilterOn method Eric Coissac 2022-08-21 15:05:14 +02:00
• ad4a861261 Change some comments Eric Coissac 2022-08-21 14:47:22 +02:00
• 10663bf79c Patch an algorithm error on th Annotation Classifier Eric Coissac 2022-08-21 14:45:53 +02:00
• f1e3a68dc4 improved performance Eric Coissac 2022-08-21 13:44:09 +02:00
• 02f445f02f same as previous commit Eric Coissac 2022-08-21 13:43:27 +02:00
• 34e957d3fb Add an option alowwing to use the pool method instead of the concat method when several input files are specified Eric Coissac 2022-08-21 13:43:00 +02:00
• 844e24b818 Add information on the number of workers in the log Eric Coissac 2022-08-21 13:41:58 +02:00
• f00456fcf3 Add a second way to merge several batch iterators using the pool method. Eric Coissac 2022-08-21 13:41:15 +02:00
• 3e40ae9d52 Patch a memory leak in apat sequence Eric Coissac 2022-08-21 13:40:20 +02:00
• 9677f531c4 Improved performance and ability to read very long sequences. Eric Coissac 2022-08-21 13:38:13 +02:00
• 5dd835d3e7 A first functional version of obiclean Eric Coissac 2022-08-20 18:01:07 +02:00
• a07d348aea small change Eric Coissac 2022-07-31 21:52:04 +02:00
• 821abb1395 package obistat debut Eric Coissac 2022-07-28 16:52:27 +02:00
• b4cabf31fc Correctly print StatsOn values in obiformat style Eric Coissac 2022-06-14 10:00:45 +02:00
• f0de4d8f28 Finalize the correct merging of statistic of occurrences, in I expect every situation Eric Coissac 2022-06-14 09:54:33 +02:00
• 6b13729eba Adds a test for not pushing empty batch on the output Eric Coissac 2022-06-14 09:53:35 +02:00
• cf5b4baa54 Small bug in sequence counting on merge Eric Coissac 2022-05-30 16:28:59 +02:00
• f14860a486 Patch header parting and formatiing Eric Coissac 2022-05-27 11:53:29 +03:00
• 656eda1f73 A fiirst version of LCS score function Eric Coissac 2022-03-07 16:37:21 +01:00
• 62cd1c44dc Corrects some bug in building the sequence filter Eric Coissac 2022-02-25 10:36:01 +01:00